As ontologies evolve, the ability to discover how they have changed over time becomes critical. In the recent past, a handful of useful tools based on the Manchester OWL API have addressed this issue. However, none of these tools took into account how to align entities across ontologies when the names of entities have changed. For the case of name changes, we need a way to discover entity alignments between two ontology versions before we can match up structural differences. In this paper, we describe a highly optimized pluggable difference engine that searches for alignments between entities in different ontology versions and applies those alignments to display the differences in the ontologies. This difference engine is available as a plug-in in the latest Protege 4.2 release and sources are available online.1 We discuss our experiences applying the tools to a selection of ontologies from the BioPortal  ontology repository, including the performance and accuracy of the tool.